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Hps4 HPS4, biogenesis of lysosomal organelles complex 3 subunit 2 [ Rattus norvegicus (Norway rat) ]

Gene ID: 304555, updated on 4-Jan-2025

Summary

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Official Symbol
Hps4provided by RGD
Official Full Name
HPS4, biogenesis of lysosomal organelles complex 3 subunit 2provided by RGD
Primary source
RGD:1308070
See related
EnsemblRapid:ENSRNOG00000000661 AllianceGenome:RGD:1308070
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable protein homodimerization activity and small GTPase binding activity. Predicted to contribute to guanyl-nucleotide exchange factor activity. Predicted to be involved in several processes, including melanosome assembly; positive regulation of protein targeting to mitochondrion; and protein stabilization. Predicted to act upstream of or within blood coagulation and melanocyte differentiation. Predicted to be located in cytoplasmic vesicle; lysosome; and membrane. Predicted to be part of BLOC-3 complex. Predicted to be active in cytoplasmic vesicle and lysosomal membrane. Human ortholog(s) of this gene implicated in Hermansky-Pudlak syndrome; Hermansky-Pudlak syndrome 4; and schizophrenia. Orthologous to human HPS4 (HPS4 biogenesis of lysosomal organelles complex 3 subunit 2). [provided by Alliance of Genome Resources, Jan 2025]
Expression
Biased expression in Brain (RPKM 30.7), Kidney (RPKM 29.0) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Hps4 in Genome Data Viewer
Location:
12q16
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (49924444..49955201, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (44264037..44294791, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (50285239..50315893, complement)

Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene seizure related 6 homolog like Neighboring gene coiled-coil domain containing 121 like 2 Neighboring gene aspartate beta-hydroxylase domain containing 2 Neighboring gene coiled-coil domain-containing protein 121-like Neighboring gene tuftelin interacting protein 11 Neighboring gene SRR1 domain containing Neighboring gene tyrosylprotein sulfotransferase 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Hermansky-Pudlak syndrome type 4 (HPS-4): clinical and molecular characteristics. Anderson PD, et al. Hum Genet, 2003 Jul. PMID 12664304
  2. An association study of the Hermansky-Pudlak syndrome type 4 gene in schizophrenic patients. Saito A, et al. Psychiatr Genet, 2013 Aug. PMID 23563589
  3. BLOC-3, a protein complex containing the Hermansky-Pudlak syndrome gene products HPS1 and HPS4. Martina JA, et al. J Biol Chem, 2003 Aug 1. PMID 12756248
  4. The Hermansky-Pudlak syndrome 1 (HPS1) and HPS4 proteins are components of two complexes, BLOC-3 and BLOC-4, involved in the biogenesis of lysosome-related organelles. Chiang PW, et al. J Biol Chem, 2003 May 30. PMID 12663659
  5. Assembly of the biogenesis of lysosome-related organelles complex-3 (BLOC-3) and its interaction with Rab9. Kloer DP, et al. J Biol Chem, 2010 Mar 5. PMID 20048159, Free PMC Article

See all (12) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
contributes_to guanyl-nucleotide exchange factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to guanyl-nucleotide exchange factor activity ISO
Inferred from Sequence Orthology
more info
  
enables protein dimerization activity ISO
Inferred from Sequence Orthology
more info
  
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
  
enables small GTPase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables small GTPase binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
acts_upstream_of_or_within blood coagulation ISO
Inferred from Sequence Orthology
more info
  
involved_in lysosome organization ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within melanocyte differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in melanosome assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in melanosome assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of protein targeting to mitochondrion ISO
Inferred from Sequence Orthology
more info
 PubMed 
involved_in protein stabilization ISO
Inferred from Sequence Orthology
more info
  
involved_in protein targeting IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein targeting ISO
Inferred from Sequence Orthology
more info
  
involved_in vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of BLOC-3 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of BLOC-3 complex ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in cytoplasmic vesicle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasmic vesicle ISO
Inferred from Sequence Orthology
more info
  
is_active_in lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in lysosome ISO
Inferred from Sequence Orthology
more info
  
located_in melanosome ISO
Inferred from Sequence Orthology
more info
  
located_in membrane ISO
Inferred from Sequence Orthology
more info
  
located_in platelet dense granule ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
BLOC-3 complex member HPS4
Names
Hermansky-Pudlak syndrome 4 homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001107148.3 → NP_001100618.2  BLOC-3 complex member HPS4

    See identical proteins and their annotated locations for NP_001100618.2

    Status: VALIDATED

    Source sequence(s)
    BC168901, JAXUCZ010000012
    UniProtKB/TrEMBL
    A0A8J8YPH6
    Related
    ENSRNOP00000071892.3, ENSRNOT00000079256.3
    Conserved Domains (3) summary
    PHA03307
    Location:225 → 490
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam19031
    Location:15 → 121
    Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
    pfam19033
    Location:551 → 652
    Intu_longin_3; Intu longin-like domain 3

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086030.1 Reference GRCr8

    Range
    49924444..49955201 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039089506.2 → XP_038945434.1  BLOC-3 complex member HPS4 isoform X1

    UniProtKB/TrEMBL
    A0A8J8YPH6
    Conserved Domains (3) summary
    PHA03307
    Location:225 → 490
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam19031
    Location:15 → 121
    Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
    pfam19033
    Location:551 → 652
    Intu_longin_3; Intu longin-like domain 3

  2. XM_006249544.4 → XP_006249606.1  BLOC-3 complex member HPS4 isoform X1

    See identical proteins and their annotated locations for XP_006249606.1

    UniProtKB/TrEMBL
    A0A8J8YPH6
    Conserved Domains (3) summary
    PHA03307
    Location:225 → 490
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam19031
    Location:15 → 121
    Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
    pfam19033
    Location:551 → 652
    Intu_longin_3; Intu longin-like domain 3

  3. XM_006249542.5 → XP_006249604.1  BLOC-3 complex member HPS4 isoform X1

    See identical proteins and their annotated locations for XP_006249604.1

    UniProtKB/TrEMBL
    A0A8J8YPH6
    Conserved Domains (3) summary
    PHA03307
    Location:225 → 490
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam19031
    Location:15 → 121
    Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
    pfam19033
    Location:551 → 652
    Intu_longin_3; Intu longin-like domain 3

  4. XM_063271364.1 → XP_063127434.1  BLOC-3 complex member HPS4 isoform X2

    UniProtKB/TrEMBL
    A0A0G2K1L6

  5. XM_006249546.5 → XP_006249608.1  BLOC-3 complex member HPS4 isoform X3

    UniProtKB/TrEMBL
    A0A0G2K1L6
    Conserved Domains (1) summary
    PHA03307
    Location:225 → 490
    PHA03307; transcriptional regulator ICP4; Provisional

  6. XM_039089507.2 → XP_038945435.1  BLOC-3 complex member HPS4 isoform X4

    UniProtKB/TrEMBL
    A0A0G2K1L6
    Conserved Domains (2) summary
    PHA03307
    Location:225 → 490
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam19031
    Location:15 → 121
    Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4

  7. XM_006249543.5 → XP_006249605.1  BLOC-3 complex member HPS4 isoform X1

    See identical proteins and their annotated locations for XP_006249605.1

    UniProtKB/TrEMBL
    A0A8J8YPH6
    Conserved Domains (3) summary
    PHA03307
    Location:225 → 490
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam19031
    Location:15 → 121
    Intu_longin_1; First Longin domain of INTU, CCZ1 and HPS4
    pfam19033
    Location:551 → 652
    Intu_longin_3; Intu longin-like domain 3

  8. XM_063271362.1 → XP_063127432.1  BLOC-3 complex member HPS4 isoform X1

    UniProtKB/TrEMBL
    A0A8J8YPH6

  9. XM_063271363.1 → XP_063127433.1  BLOC-3 complex member HPS4 isoform X1

    UniProtKB/TrEMBL
    A0A8J8YPH6

RNA

  1. XR_358770.5 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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